Rs2542151
| Orientation | plus |
| is a | snp |
| is | mentioned by |
| dbSNP | rs2542151 |
| PheGenI | rs2542151 |
| nextbio | rs2542151 |
| hapmap | rs2542151 |
| 1000 genomes | rs2542151 |
| hgdp | rs2542151 |
| ensembl | rs2542151 |
| gopubmed | rs2542151 |
| geneview | rs2542151 |
| scholar | rs2542151 |
| rs2542151 | |
| pharmgkb | rs2542151 |
| gwascentral | rs2542151 |
| openSNP | rs2542151 |
| 23andMe | rs2542151 |
| 23andMe all | rs2542151 |
| SNP Nexus | |
| SNPshot | rs2542151 |
| SNPdbe | rs2542151 |
| MSV3d | rs2542151 |
| Gene | PTPN2 |
| Chromosome | 18 |
| Orientation | plus |
| GMAF | 0.1561 |
| Position | 12779947 |
| Reference | GRCh37 37.1/131 |
| Max Magnitude | 0 |
| Geno | Mag | Summary |
|---|---|---|
| (G;G) | 2x risk for Crohn's; 1.6x for T1D | |
| (G;T) | 1.3x risk for Crohn's; 1.3x for T1D | |
| (T;T) | 0 | normal |
| ? | (G;G) (G;T) (T;T) | 28 |
|---|---|---|
The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). [PMID 17554300]
rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). [PMID 17554300]
In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PMID 17554260]
| GWAS | |
|---|---|
| SNP | rs2542151 |
| PubMedID | [PMID 17554260] |
| Condition | Type 1 diabetes |
| Gene | PTPN2 |
| Risk Allele | C |
| pValue | 1.00E-014 |
| OR | 1.3 |
| 95% CI | 1.22-1.40 |
| GWAS snp | |
|---|---|
| PMID | [PMID 18978792] |
| Trait | Type 1 diabetes |
| Title | Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci |
| Risk Allele | C |
| P-val | 9E-8 |
| Odds Ratio | NR NR |
| GWAS snp | |
|---|---|
| PMID | [PMID 18587394] |
| Trait | Crohn's disease |
| Title | Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease |
| Risk Allele | G |
| P-val | 4.9999999999999999E-17 |
| Odds Ratio | 1.35 [NR] |
| GWAS snp | |
|---|---|
| PMID | [PMID 17554261] |
| Trait | Crohn's disease |
| Title | Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility |
| Risk Allele | |
| P-val | 2.9999999999999997E-8 |
| Odds Ratio | 1.15 [1.00-1.32] |
[PMID 19565500] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis
[PMID 19953089] Differences in genetic background between active smokers, passive smokers, and non-smokers with Crohn's disease
[PMID 21246196] A polymorphism in PTPN2 gene is associated with an earlier onset of type 1 diabetes
| GWAS snp | |
|---|---|
| PMID | [PMID 21829393] |
| Trait | |
| Title | Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. |
| Risk Allele | G |
| P-val | 4E-13 |
| Odds Ratio | 1.3000 [NR] |
[PMID 22377701] PTPN2 is associated with Crohn's disease and its expression is regulated by NKX2-3.
[PMID 18224312] Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.
[PMID 18252225] On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.
[PMID 18423522] Estimating odds ratios in genome scans: an approximate conditional likelihood approach.
[PMID 18438406] Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.
[PMID 18533027] Worldwide population differentiation at disease-associated SNPs.
[PMID 18853133] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.
[PMID 19140132] Unbiased estimation of odds ratios: combining genomewide association scans with replication studies.
[PMID 19359276] Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.
[PMID 19474294] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
[PMID 19639606] Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases.
[PMID 19776214] SimCT: a generic tool to visualize ontology-based relationships for biological objects.
[PMID 19915572] Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
[PMID 20369022] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
[PMID 20403149] PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population.
[PMID 21304977] An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians.
[PMID 22021207] Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.
[PMID 22426692] Confirmation of three inflammatory bowel disease susceptibility loci in a Chinese cohort.
| GET Evidence | |
|---|---|
| rs2542151 | |
| aa_change | |
| aa_change_short | |
| impact | pathogenic |
| qualified_impact | Insufficiently evaluated pathogenic |
| overall_frequency | 0.898438 |
| summary | |
